%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#B6ECE2',
      'primaryTextColor': '#160F26',
      'primaryBorderColor': '#065647',
      'lineColor': '#545555',
      'clusterBkg': '#BABCBD22',
      'clusterBorder': '#DDDEDE',
      'fontFamily': 'arial'
    }
  }
}%%
flowchart TB
    subgraph " "
    v2["Channel.fromList"]
    v7["Channel.fromPath"]
    v93[" "]
    v139["Channel.of"]
    v142["Channel.fromPath"]
    v145["ch_workflow_summary"]
    v149["ch_methods_description"]
    v161["replace_names"]
    v162["sample_names"]
    end
    subgraph "NFCORE_METHYLSEQ [NFCORE_METHYLSEQ]"
    subgraph "NFCORE_METHYLSEQ:FASTA_INDEX_BISMARK_BWAMETH [FASTA_INDEX_BISMARK_BWAMETH]"
    v19(["GUNZIP"])
    v22(["BISMARK_GENOMEPREPARATION"])
    v18(( ))
    v21(( ))
    end
    subgraph "NFCORE_METHYLSEQ:METHYLSEQ [METHYLSEQ]"
    v47(["CAT_FASTQ"])
    v50(["FASTQC"])
    subgraph "NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK [FASTQ_ALIGN_DEDUP_BISMARK]"
    v85(["BISMARK_ALIGN"])
    v90(["BISMARK_DEDUPLICATE"])
    v94(["SAMTOOLS_SORT"])
    v99(["SAMTOOLS_INDEX"])
    v104(["BISMARK_METHYLATIONEXTRACTOR"])
    v108(["BISMARK_COVERAGE2CYTOSINE"])
    v115(["BISMARK_REPORT"])
    v123(["BISMARK_SUMMARY"])
    v87(( ))
    v89(( ))
    v91(( ))
    v117(( ))
    v121(( ))
    v122(( ))
    end
    v163(["MULTIQC"])
    v46(( ))
    v49(( ))
    v158(( ))
    v159(( ))
    v160(( ))
    v167(( ))
    end
    v8(( ))
    v24(( ))
    end
    subgraph " "
    v51["ch_fastqc_html"]
    v86[" "]
    v88["ch_alignment_reports"]
    v95[" "]
    v96[" "]
    v97[" "]
    v100[" "]
    v101[" "]
    v102["bai"]
    v105["methylation_calls"]
    v106["ch_bedgraph"]
    v109["coverage2cytosine_summary"]
    v110["coverage2cytosine_report"]
    v111["coverage2cytosine_coverage"]
    v164[" "]
    v165[" "]
    v166[" "]
    v169["versions"]
    v171[" "]
    end
    subgraph "PIPELINE_INITIALISATION [PIPELINE_INITIALISATION]"
    v3(( ))
    end
    subgraph "PIPELINE_COMPLETION [PIPELINE_COMPLETION]"
    v170(( ))
    end
    v2 --> v3
    v7 --> v8
    v18 --> v19
    v19 --> v18
    v19 --> v21
    v18 --> v22
    v22 --> v21
    v22 --> v46
    v46 --> v47
    v47 --> v46
    v47 --> v49
    v46 --> v50
    v50 --> v51
    v50 --> v49
    v46 --> v85
    v85 --> v90
    v85 --> v86
    v85 --> v87
    v85 --> v89
    v85 --> v91
    v85 --> v117
    v87 --> v88
    v90 --> v94
    v90 --> v104
    v90 --> v89
    v90 --> v91
    v93 --> v94
    v94 --> v99
    v94 --> v97
    v94 --> v96
    v94 --> v95
    v94 --> v89
    v99 --> v102
    v99 --> v101
    v99 --> v100
    v99 --> v89
    v46 --> v104
    v104 --> v106
    v104 --> v105
    v104 --> v108
    v104 --> v89
    v104 --> v91
    v104 --> v121
    v104 --> v122
    v46 --> v108
    v108 --> v111
    v108 --> v110
    v108 --> v109
    v108 --> v89
    v91 --> v115
    v115 --> v89
    v115 --> v91
    v91 --> v123
    v117 --> v123
    v121 --> v123
    v122 --> v123
    v123 --> v89
    v123 --> v91
    v139 --> v49
    v142 --> v158
    v145 --> v49
    v149 --> v49
    v161 --> v163
    v162 --> v163
    v49 --> v163
    v158 --> v163
    v159 --> v163
    v160 --> v163
    v163 --> v166
    v163 --> v165
    v163 --> v164
    v163 --> v167
    v24 --> v169
    v170 --> v171
    v3 --> v46
    v8 --> v18
    v18 --> v46
    v21 --> v24
    v49 --> v24
    v24 --> v49
    v89 --> v49
    v91 --> v49
    v167 --> v170